Question

What are out-of-bound ranges? Is it necessary to get rid of them?

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salamandra ▴ 20

@salamandra-12825

Last seen 2.3 years ago

Portugal

With the function:

overlaps.anno <- annotatePeakInBatch(overlaps, AnnotationData=annoData, output="nearestBiDirectionalPromoters",bindingRegion=c(-2000, 500))

got this warning message:

Annotate peaks by annoPeaks, see ?annoPeaks for details.
maxgap will be ignored.
Warning messages:
1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 5 out-of-bound ranges located on sequences GL000199.1 and
  chrM. Note that only ranges located on a non-circular sequence whose length is not
  NA can be considered out-of-bound (use seqlengths() and isCircular() to get the
  lengths and circularity flags of the underlying sequences). You can use trim() to
  trim these ranges. See ?`trim,GenomicRanges-method` for more information.

What are the out-of-bound ranges? Is it advisable that we get rid of them?

r ChIPpeakAnno • 4.7k views

ADD COMMENT • link 7.0 years ago • updated 6.8 years ago salamandra ▴ 20

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Please tag your message with the package name, ChIPpeakAnno, so the author is aware of the question.

ADD REPLY • link updated 7.0 years ago by Martin Morgan 25k • written 7.0 years ago by Valerie Obenchain ★ 6.8k

score 4 · Accepted Answer · 2017-04-21

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Julie Zhu ★ 4.3k

@julie-zhu-3596

Last seen 5 months ago

United States

The out-of-bound ranges are ranges that are not valid coordinates in the chromosome. The warning message indicates that there are 5 such ranges in chrM and GL000199.1 from your data (overlaps). You can use trim(overlaps) instead of overlaps as input for annotatePeakInBatch. Here is a nice post to locate ranges that are out of bound https://www.biostars.org/p/98315/.

Best regards,

Julie

ADD COMMENT • link 7.0 years ago Julie Zhu ★ 4.3k

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Thanks Julie for the nice explanation. A couple of comments about the Biostar answer:

The seqlengths are stored in the GRanges object so there is no need to use a BSgenome package to get them. Therefore

which(end(mygr) > seqlengths(BSgenome.Hsapiens.UCSC.hg19)[as.character(seqnames(mygr))])

can be replaced with

which(end(mygr) > seqlengths(mygr)[as.character(seqnames(mygr))])

Note that ranges are considered out-of-bound only if the GRanges object contains the seqlengths information. If it doesn't contain the seqlengths information or contains it for some sequences only, the vectorized comparison (>) in the above code will generate NAs. However which() will ignore them so we're good.

Another thing is that in some rare situations, some ranges can start at a position < 1. These ranges are also considered out-of-bound. So a more accurate version of the above code would be something like

seqends <- seqlengths(mygr)[as.character(seqnames(mygr))]
which(start(mygr) < 1L | end(mygr) > seqends)

Finally ranges defined on a circular sequence (e.g. chrM) are never considered out-of-bound. So a completely accurate version of the above code would be even more complicated. It's actually implemented in internal utility GenomicRanges:::get_out_of_bound_index() which is used internally by the validity and "trim" methods for GRanges objects.

All this to say that the easiest and most reliable way of getting the index of out-of-bound ranges is probably to do which(mygr.original != mygr.trimmed), as suggested in the Biostar answer.

Cheers,

H.

ADD REPLY • link 7.0 years ago Hervé Pagès 16k

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Herve, Thanks for such a thorough discussion on this topic! Best regards, Julie From: "Herv� Pag�s [bioc]" <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> Reply-To: "reply+9b1b6cf2+code@bioconductor.org<mailto:reply+9b1b6cf2+code@bioconductor.org>" <reply+9b1b6cf2+code@bioconductor.org<mailto:reply+9b1b6cf2+code@bioconductor.org>> Date: Friday, April 21, 2017 3:18 PM To: Lihua Julie Zhu <julie.zhu@umassmed.edu<mailto:julie.zhu@umassmed.edu>> Subject: [bioc] C: What are out-of-bound ranges? Is it necessary to get rid of them? Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User Herv� Pag�s<https: support.bioconductor.org="" u="" 1542=""/> wrote Comment: What are out-of-bound ranges? Is it necessary to get rid of them?<https: support.bioconductor.org="" p="" 94851="" #95158="">: Thanks Julie for the nice explanation. A couple of comments about the Biostar answer: The seqlengths are stored in the GRanges object so there is no need to use a BSgenome package to get them. Therefore which(end(mygr) > seqlengths(BSgenome.Hsapiens.UCSC.hg19)[as.character(seqnames(mygr))]) can be replaced with which(end(mygr) > seqlengths(mygr)[as.character(seqnames(mygr))]) Note that ranges are considered out-of-bound only if the GRanges object contains the seqlengths information. If it doesn't contain the seqlengths information or contains it for some sequences only, the vectorized comparison (>) in the above code will generate NAs. However which() will ignore them so we're good. Another thing is that in some rare situations, some ranges can start at a position < 1. These ranges are also considered out-of-bound. So a more accurate version of the above code would be something like seqends <- seqlengths(mygr)[as.character(seqnames(mygr))] which(start(mygr) < 1L | end(mygr) > seqends) Finally ranges defined on a circular sequence (e.g. chrM) are never considered out-of-bound. So a completely accurate version of the above code would be even more complicated. It's actually implemented in internal utility GenomicRanges:::get_out_of_bound_index() which is used internally by the validity and "trim" methods for GRanges objects. All this to say that the easiest and most reliable way of getting the index of out-of-bound ranges is probably to do which(mygr.original != mygr.trimmed), as suggested in the Biostar answer. Cheers, H. ________________________________ Post tags: r You may reply via email or visit C: What are out-of-bound ranges? Is it necessary to get rid of them?

ADD REPLY • link 7.0 years ago Julie Zhu ★ 4.3k